04 150 Yamaha 4 stroke skips

The motor has a skip when cold. Most of the time it only last few minutes. This started last fall. I have changed the water fuel separator and surely run enough gas thru it to clear out any water in the gas. IT seems like one cylinder is missing. I ran it for three days this weekend and it only did it on the first day. It only does this when it sits for a week or more.
Any ideas???

Not the same I’m sure but my coil on plug ford truck engine did the same… After sitting or rain. Moisture got in from a Leakey hood gasket dripping on a plug. Pulled it out some silicone spray and fixed the leak. Good as new… My 2 cents, maybe moisture in something electrical then cooks it out when hot